KEGGtranslator 2.5

Improvements in version 2.5

New features:

• Support for SBML Level 2 Version 5
• Use of identifiers.org URIs (uniform resource identifiers) instead of URNs (uniform resource names)
• Support for the flux balance constraints (FBC) package version 2 for SBML: KEGGtranslator now writes the chemical formula into species when converting to Level 3 Version 1.
• Improved user interface with support for more SBML package elements and their attributes
• Update to the latest repository version 1.1 of JSBML, revision 2358
• Produced SBML files have now a correct indentation.

Bug fixes:

• Correct use of the SBML groups extension:
  • In some cases, KEGGtranslator created duplicate identifiers that could not be added to the model.
  • Elements were not correctly linked to group members
• In situations when a link to KEGG containes special characters, such as colons, JSBML refuses writing those in the notes element and throws an exception. As a result, KEGGtranslator crashed. Special characters are now masked in these links.
• Additional code has been added to catch potential excaptions and to hence make the program more stable.